To Study Nature

-By Georges Cuvier, Henry M'Murtrie

Possible Longest Wrong Number Ever!

Generally, text messaging speeds up communication.  You can say succincltly what you want and get on with your day while you wait for an answer.  Yet text messaging has also made it so that a simple wrong number has become a gigantic hassle.  This is how the texting went:

Unknown Number: Heyy what are you doing =-)

Me: Who is this?

Unknown: Dang how many girls do you give your number that you can't remember?

Me: my phone isn't showing a name so all I can tell is it's a person in or from Calif.

Unknown: oh remember we met last weekend when you got off work and we went out and got drunk =-)

Me: No, you have the wrong number. I'm in TN and haven't been out in a while

Unknown: no I don't this is bibi right

I don't like wrong numbers.  I don't like it when people play games to make you guess who it is on the phone because they somehow think they're special and I especially don't like being told I'm wrong when I know I'm not.  Consiquently, I called the number so I could resolve the issue once and for all.  That went roughly as follows:

Me: Hello

Unknown: Hey, what's going on?

Me:  You've been texting me today and I want to let you know you've got the wrong number.

Unknown: Well, what number is it?

Me: 714 (767- ####)

Unknown: Hey, just a sec, let me check (continues conversation with person in the room with her).  No, that's the right number.  This is Bibi right?

Me:  No, I'm telling you.  I'm not Bibi and I don't know how you got my number but you either misdialed originally or something!

Unknown: Oh come on Bibi, why you got to be like that?

Me:  Why do you refuse to believe me?!  I'm not Bibi, I don't know any such person and even if I was Bibi, you should have taken this as a hint a long time ago that either way, I don't want to be hearing from you!  You've got the wrong frickin' number.  Don't text me again.

The first text was at about noon.  The end of the conversation was at about 6:30 in the evening.  A six and a half hour wrong number has to be close to some kind of record.

Bird puns

People hate my puns, I know, 

and so on the internet they shall go.

to see these puns you might

have intentionally visited a pun filled site

The American Museum's collection of birds

have provided woodpecker puns, abundant, absurd.  

The woodpecker, a two part name; phallic each.

Dryobates one resorts to when lube's far from reach.

The downy woodpecker is Picoides pubescens 

Though calling the hairy woodpecker, one could easily defend

And though this verse could get much sicker

One gets no Melanerpes when one Dryobates,

But do beware the Flicker

I am a paleontologist

The awesome alternative rock band "They Might Be Giants"  has a new science themed album out and one of the songs is titled "I am a Paleontologist."  The lyrics are as follows:

I love diggin' in the dirt 
With just a pick and brush 
Finding fossils is my aim 
So I'm never in a rush 
'Cause the treasures that I seek 
Are rare and ancient things 
Like Velociraptor's jaw 
Or Archaeopteryx's wings 

Now all the kids 
Who wanna see 'em 
Are lining up 
At our museum 

I am a paleontologist 
That's who I am, that's who I am, that's who I am 
I am a paleontologist 
That's who I am, that's who I am, that's who I am 

Could it be an herbivore 
Crushing plants with rounded teeth 
Or ferocious carnivore 
Who moves so quickly on its feet 
It's like pieces of a puzzle 
That I love to try and solve 
It's so fun to think about 
How a species has evolved 

And all the kids 
Who wanna see 'em 
Can check 'em out 
At our museum 

I am a paleontologist 
That's who I am, that's who I am, that's who I am 
I am a paleontologist 
That's who I am, that's who I am, that's who I am 

Is it a T-rex? (I keep digging, digging, digging, digging) 
(Digging, digging, digging, digging) 
Maybe a Triceratops? (Digging, digging, digging, digging) 
(Digging, digging, digging, digging) 
Or a Carnotaur? (Digging, digging, digging, digging) 
(Digging, digging, digging, digging) 
(Digging, digging, digging, digging, diggin') 
Pachycephalosaurus? 

I am a paleontologist 
That's who I am, that's who I am, that's who I am 
I am a paleontologist 
That's who I am, that's who I am, that's who I am 
That's who I am, that's who I am, that's who I am 
That's who I am, that's who I am, that's who I am

Hidden Treasure

I hid a quartz crystal and a note behind the mirror when my sister remodeled the bathroom.  It's my hope that someday, somebody else remodels the bathroom and gets a kick out of finding hidden treasure and an old-school video game reference. In case you can't read the small print.  The note says "Congratulations, you found the treasure but the princess is in another castle."

Hermitage

For a hermit, the choice of one's hermitage is not the most important of things.  A place is a place so long as one is comfortable.  However, some hermitages stand out from others as having exceptional taste, even by hermits' standards, which may be regarded as significantly higher than the next persons (why do you think we spend so much time away from the next person?).  I've decided that if given the choice, I think I'd like the Hermitage Museum in St Petersburg.  The weather certainly could be better, but I think that the decor makes up for it.  I think that with that hermitage and the occasional company of an intelligent and beautiful woman, I could be truly happy for a while.  With over 15 miles of art galleries I could certainly fill my days with pleasant walks even on the colder days.

Quotes du jour

said earlier today over coffee:

"trying to get your all the facets of your life together is like grasping at straws being blown in the wind off three different hay bails."

&

"By the time you get your life together, you're probably too old to care."

The Death of the Social E-mail

Remember the good old days when you had to actually write a letter, on paper, put a stamp on the envelope and wait a week just to send a friendly 'hello' to someone you haven't heard from in a while?  No?  Good, then you were born some time after the invention of the telephone.  Writing letters for more than formal announcements made a come-back with the advent of e-mail.  Being free and instantaneous meant people could frivolously spend their time personally catching up with old friends on a one by one basis.  Then came blogs, and social networking sites and microblogs (ie. twitter).  I'll admit that I'm somewhat behind for commenting on this now (after all, even Led Zeppelin is still pretty new to me), but I see the death of social e-mail even affecting my own interactions now.  Some of my best friends are people I talk to a couple of times a year.  If our daily activities don't overlap, odds are we don't have any banalities to sit around and talk about.  Since it's the banalities that tend to lead into the bigger topics, I just end up talking about whatever big events have happened.  For the rest of the time, I can just check your status, mood, interests (new and old) and catch up via your archives.  People just don't have an excuse to ask 'So, what's going on with you' any more.  Therefore, e-mail, just like postal mail, shall be relegated to formal announcements to select groups of people or else the highly personal stuff that people are too afraid to say either in person or over the phone.

Immunity Challenge

I'm sick of Tennessee, I'm sick in Tennessee.  This summer has so far exceeded all others for days I've been sick while the weather is nice.  In mid May I came down with a soar throat and cough that persisted for over a week and led me to go to the campus clinic to get a Strep test.  Although the rapid Strep test (which only tests for strain A) came back negative, the doctor prescribed antibiotics anyway.  Sure enough, the soar throat and cough went away.  I took the pills for 10 days and finished off the prescription, then I got really sick.  Without going into too much graphic detail, I ended up going back to the doctor, getting blood and urine tests done and being told that Mono and Hepatitis were the two diseases that he though were most likely, but neither explained the bile in my urine.  For my time at the doctor's office, I got nothing but a bill and an appointment for next Wednesday to go over my liver function assay and possibly do more tests.  

The next day after that, my gums somehow got infected, then the sore throat came back and then just about everything went away.  I'm still not back to 100% health, but I feel much better, especially after two or three cups of coffee.  I feel like a human being again rather than a walking disease vector.

I suspect that the antibiotics were the cause of all the problems.  Possibly they disturbed the balance of my usually varied and hardy bacterial flora.  There were probably lots of very low concentration bacteria that performed specific jobs and kept each other in check as well as kept out new, competing pathogens.  Once one or two microbes were allowed to become dominant, they wrecked havoc on my body, and it wasn't been till now that my body is getting things back in check.  Clearly my body is just too fragile to handle modern medicine.

SLEEEEEEEEP!

My bed is now just for show.  Having mastered procrastination in high school and producing quality work in the AM in my Undergrad, I've finally conquered the last hurtle, sleep itself.  I'm not sure how long I can keep going like this, but I've had a total of 9 hours of sleep since Sunday, 4 days ago.  In the past I'd always gone through several predictable stages of exhaustion: aches, difficulty staying alert, eventually hallucinations (rare).  This time though, I have yet to really experience any of that.  I've been a little crankier, but hanging out with Kristina fixes that right away.  My hourly productivity is a little down too, but with so many extra hours, I'm just plugging away.  The body keeps moving, the projects and assignments get finished, and so the academic robot is complete.

Inclusive fitness

The theory of inclusive fitness argues that a gene for altruistic behavior will increase in a population when the reward for the altruism, proportional to the degree of relatedness of a recipient, is greater than the cost to oneself.  The problem with this is that traditional methods of measuring relatedness would say that each parent, offspring and sibling all have an r-value of 0.5.  That is, there is a 50% chance that any given gene that you share is via common ancestry.  That is, it is equally advantageous to help a parent, a sibling or offspring.  However, in terms of human examples, I think that a parent would be willing to make a sacrifice for their child more readily than for their sibling or parent.  Altruism toward individuals with an r value of 0.5 is common in females of a social species.  In many cases, there is help between sisters or mothers and daughters or even aunt and niece, but I'm fairly confident that it is much more common to see males only their parent, or less commonly their sibling or offspring.  I think that the reason for this is that the male is geared for more of what will be the next generation result of his help.  A parent can produce another sibling so that the inclusive fitness is increased by another individual of r=0.5, whereas helping a sibling or offspring produces individuals of r=0.25.  Therefore, I would expect that you would see male helpers of their parents at a certain rate in monogamous species, and about half as commonly for a parent in non-monogamous species and for either siblings or offspring.  

The Samurai and the Monk

In ancient Japan, one monk had the reputation of being the greatest cook in the entire Empire.  A samurai, similarly reputed for his excellence as a warrior, heard of this and journeyed to the monastery where he hoped to dine on as fine a repast as befit his status.  The monastery, like most monasteries that people of great importance reside in, was situated at the top of a great mountain.  Leaving his horse, for the slope was too steep, the samurai climbed the 5 thousand steps to the gates of the temple.  Once inside, he announced his presence and respectfully requested that the monk of famous culinary abilities, prepare a meal for him.  He was lead to a wide room with a single low table and was told that the great cook would be with him shortly.  Soon, a small, elderly man with a worn and wizened face entered and greeted the samurai.  “I am the cook which you seek” said the old man.  “I am humbled that a great warrior such as yourself would honor me with a request for a dish prepared by my hand.”

“Monk, I have traveled far to taste the most delicious food in the empire.  Bring me what you will, for your reputation is so great that I trust your judgment” replied the samurai.  At this, the monk bowed low and said “I know just the thing, but it will take some time to prepare.  I hope that you will be patient.”  The samurai agreed and the monk exited.  Hours passed with no sign of the monk’s return and the stomach of the samurai increasingly made its presence known to its owner.  The samurai asked any monk he saw if they knew when the great cook would return.  He meditated a while, but was interrupted by pangs of hunger.  Just as the samurai was fomenting into a ravenous fit, the great monk reappeared with a tray bearing a bowl of soup.  The samurai leapt at the bowl, and swiping it from the tray, raised it to his mouth and drained it without stopping for breath, spilling not a drop. 

“The legends are true!” exclaimed the samurai.  “That is the most exquisite, delicious soup that I have ever tasted!  It is as though this soup gives me new life! Before you bring anything else, I must know the secret of making such a soup so that my servants can prepare it at home so that I may be so rejuvenated after battle, if not daily.”

The monk smiled and bowed low.  He raised back up and explained to the samurai that it was in fact the only course and was actually a simple miso soup; that anticipation, and hunger was the spice that made the soup wonderful.  Had he not expected that he would enjoy it, or gone so long without food of any kind for so long, objective observation would show it to be as good as that of any other cook.  The samurai thought on this for a moment and then thanked the monk for imparting on him such wisdom and causing him to realize that he really wanted food cooked well not necessarily delicious food.  He then slew the monk for so wasting his valuable time and making him into a parable without prior consent.  For good measure, he proceeded to slaughter the rest of the monks in the monastery, lest they try this sort of thing again.  Half way through the slaughter, a half dead monk fell at the feet of the samurai and pleaded “but was it not the most delicious soup you ever tasted?”

“Yes” replied the samurai flatly “but I will now question my enjoyment of anything else that I encounter in life.  I will never again enjoy food so much as I did that soup, I will never enjoy anything so much as I once have.”  The monk at his feet had an excellent reply but expired before being able to retort.

Etymology

I can't believe that I never thought to look up the etymology of 'Hermit' before.  Here it is from the Online Etymology Dictionary :

1130, from O.Fr. (h)eremite, from L.L. ermita, from Gk. eremites, lit. "person of the desert," from eremia "desert, solitude," from eremos"uninhabited." 

I had hoped that it had something to do with the solitary habits of those who traveled and would therefore have the patron god Hermes.  It still seems exceptionally appropriate that it refers to desert dwellers.  I've always felt most at home in the desert.  I think that I'll perpetuate the misnomer that has to do with Hermes as well, that way I can have the best of both origins.

Haekel's Drawings

Apparently someone cut out each of Ernst Haekel's drawing of invertebrates and put them online under a creative commons license.  Awesome!!!

Check out the gallery Here

A Life Without Holidays

This weekend was Valentine's Day, which got me thinking about holidays and other date/ purpose specific celebrations.  I've written previously about my general dislike for obliged gift giving and reciprocation thereof, but this time I think that I'll assail holidays in general.  

Scrooge was taught to keep Christmas in his hearth throughout the year.  The same principal could be applied to any holiday.  If you are in a relationship, keep Valentine's day in your heart throughout the year.  The holiday and the traditions associated with it are there as a reminder to perform acts and displays of affection and devotion, because frankly people forget.  Listening to the Dr. Laura radio show, the majority of callers looking for help are advised to overtly show their lover that they care about them.  That alone seems to resolve tons of relationship issues.  Holidays and their traditions are there as reminders that serve some social function, whether it is to strengthen family bonds (however often it actually works is up in the air) at Thanksgiving, give people an excuse to dress up an express themselves in disguise at halloween, promote altruism at Christmas.

But this is the twenty first century!  Aren't we as a society and as individuals above the necessity of tradition?  Once we know the purpose of the tradition, can't we find a suitable substitute for it that doesn't oblige us to the limitations that having a holiday on a specific date presents us?  If a husband tells his wife that he loves her on their anniversary, it won't make up for not saying it the rest of the year, but not saying it on that day has bigger consequences than not saying it any other day because of the importance of the calendar date, not the sentiment.  Essentially, having the reminder on a specific date, and then associating importance with that date is deleterious to the intent of the holiday.  Celebrating keeps you at status quo while not celebrating costs you something.

If we were to switch to a system where there were year round public reminders of the virtues espoused by our holidays, would people actually apply those virtues more?  Sadly, I doubt it.  People would just learn to ignore the reminders, staying at the status quo all year.  Having a cost associated with not exemplifying the virtue on a certain date reinforces the behavior, even if only for the period when the holiday is actively on our minds.

Sensitivity sensitivity

It occurred to me at a party the other night that the only thing that someone can say to me, that will get under my skin and raise my ire, is to call me sensitive.  

Ontology and Phylogeny

I've just read Conrad's 2008 "Phylogeny and Systematics of Squamata (Reptilia) Based on Morphology" and it has frankly left my head spinning.  What bothers me is that although this is the best attempt so far at figuring out squamate relationships, there is a big difference between the phylogeny that he developed and the one that I think is intuitively good.  I'm not saying that I prefer one evolutionary hypothesis over all others in the face of contradictory evidence, I'm saying that the distribution of characters on the tree is different from how I think a good distribution would look.  

For example, several characters that are given as unambiguous synapomorphies of a major group, are also shared with other major groups.  Iguaniamorpha, as far as I can tell is synonymous with Iguania under Conrad's taxonomy and are defined by what I consider to be mostly bad synapomorphies which include obliteration of the notochordal canal by centrum ossification, procoelous vertebrae, premaxilla fusion and possession of a ventromedial process of the pterygoids.  All of these are shared by some major schleroglossan groups!  Just about every lizard is procoelous.  Gekkotans are the only ones that I can think of that have an unossified notochort, and that is probably due to the highly derived, paedomorphic state of the group rather than an ancestral condition, something that should have been apparent from comparison to Sphenodon sp. as the outgroup.  A fused premaxilla turns up allot throughout squamate evolution: iguanians, varanids, mosasaurs, snakes, dibamus, some skinks, some geckos.  

The ventromedial process of the pterygoid is especially problematic because it not only appears in other major groups, particularly the Scincophidia (tax. nov.) and the anguinae, but it is reversed several times back and forth within the Iguania.  The Chamaeleontiformes, which includes the living acrodont iguanians and several fossil taxa is considered one of the major divisions in iguanians in other analyses has one reversal from the 'ancestral' condition and there is yet another reversal from the chamaeleontiform condition in two fossil taxa within that group.  This happens again later in the Scincophidia.  It supposedly united some derived skinks, dibamids, amphisbaenids and snakes, but dibamids don't actually have it.  This isn't the only character that does this, but I'm using it as the example.  

Intuitively, reversals from the ancestral character state shouldn't go back and forth several times in one lineage.  If it does, then there must be a strong functional correlate to it and it is therefore a highly plastic and probably bad character.  Also, characters like this popping up all over the tree would make it very hard to think of the systematics in terms of a dichotemous key.  I realize that a dichotemous key doesn't actually reflect evolutionary relationships, but if you only have one or two characters that unite big groups, it aught to at least be close or show up at some point in the creatures development.  It works for plants, birds, mammals and just about every really major group, so why not lizards?

The analysis has 363 characters and 222 ingroup taxa, so clearly this isn't a problem that is just going to be solved by throwing more characters or more taxa at it.  So what other options are there?  Character weighting or unidirectional characters?  The snakes with legs are my preferred group for this example but other groups could be used.  In the Conrad analysis, snakes fell out with other legless lizards in a clade supported by characters largely relating to enclosure of the braincase and modification of the palate.  That by itself doesn't really pose a problem except that snakes with legs, some of the oldest known fossil snakes, fall out as derived macrostomatans.  They are legged beasts nested deep within an otherwise legless group.  I find it hard to believe that they either re-evolved seemingly vestigial legs or that every other group independently lost them.  Possession of legs is such a big character that it implies that the polarity of other, more fine detail characters, is wrong.  Do you make leg possession a unidirectional character?  Weight it more than other characters?  Both of these seem wrong since the natural polarity of a character should be supported by the other characters in an analysis.  

The problem of convergence in snakes and legless lizards could be huge.  The uropeltine snakes are a very bizarre group, specialized for a very specific mode of life.  If they are a natural group, one would expect them to come out in a fairly basal position due to the sheer number of characters that they have in common with each other compared to any other member of the snakes.  If there is a single charcter that would, say unite them with Cylindrophis and 5 that unite them with each other, then Cylindrophis might be pulled out and stuck with macrostomatans because of plesiomorphies.  Establishing character polarity in a group is important but difficult, even in groups that you are certain are monophyletic.  The basal split between horned lizards (phrynosomatidae) and all other iguanians seems similar.  You have a very bizarre, highly specialized group, of unquestioned monophyly pulled out into a basal position on the phylogenetic tree.  This kind of thing could be what causes all of the character reversals higher up in the tree.

Wi11 in conversation

Ever wanted to know what the hell I was thinking when I said something?  Well now you can find out with the use of this handy flow chart of what goes on in my head during conversation.